National Repository of Grey Literature 42 records found  1 - 10nextend  jump to record: Search took 0.00 seconds. 
Mass spectrometric and optical spectroscopy studies of clusters and nanoparticles in molecular beams
Moriová, Kamila ; Fárník, Michal (advisor) ; Kopecký, Vladimír (referee)
Title: Mass spectrometric and optical spectroscopy studies of clusters and nano- particles in molecular beams Author: Kamila Moriová Institue: Institute of Physics of Charles University Supervisor: doc. Mgr. Michal Fárník, Ph.D., DSc., J. Heyrovský Institute of Phy- sical Chemistry of the CAS Consultant: RNDr. Václav Profant, Ph.D., Institute of Physics of Charles Uni- versity Abstract: Condensation of ices on the surface of dust grains with activation of these ices by cosmic rays in interstellar medium can lead to formation of complex chemical species. In the present work we primarily examine ammonia clusters, which represent a model system of ice particles. Large ammonia clusters were prepared in molecular beams and pass through a pickup chamber in which me- thanol molecules were captured. After electron ionization of (NH3)N (CH3OH)M clusters, a mass spectrum of ionic fragments was obtained in which fragments with methanol (NH3)n(CH3OH)mH+ predominated over the pure ammonia frag- ments (NH3)nH+ : at least one methanol molecule was present in 75 % fragments. This is in disproportion with the composition of the original neutral precursors, which contain less than 4 % of methanol. Based on the measurement results, we suggest that ammonia is ionized in the first place resulting in the NH+ 4 ion core solvated...
Study of protein structure and dynamics by means of optical spectroscopy
Pazderka, Tomáš ; Kopecký, Vladimír (advisor) ; Kaminský, Jakub (referee) ; Setnička, Vladimír (referee)
Title: Study of protein structure and dynamics by means of optical spectroscopy Author: Tomáš Pazderka Institute: Institute of Physics of Charles University Supervisor: RNDr. Vladimír Kopecký, Ph.D., Institute of Physics of Charles University Abstract: The aim of this thesis is to improve understanding of protein structure and dynamics and extend experimental setup and data processing for such stud- ies. We focus on the extension of experimental feasability of vibrational optical activity (VOA). We have demonstrated a usability of intensity calibration in the field of Raman optical activity. Advantages for measurements on multiple instru- ments and/or using different configurations have been shown. A new instrumental setup has been developed for microsampling measurements of vibrational circular dichroism spectra with a spatial resolution of 1 mm. Using this technique, spatial inhomogeneities in a sample of protein fibrils have been observed. Model com- pounds for amide nonplanarity have been investigated utilizing several methods of optical spectroscopy and key spectral features for determination of amide non- planarity and the absolute configuration have been identified. A comprehensive set of Raman spectra of proteinogenic amino acids has been measured. Sample concentration dependencies and consequent...
Raman spectroscopy as the tool for Alzheimer's disease diagnostics
Tesař, Adam ; Kopecký, Vladimír (advisor) ; Jelínek, Otakar (referee)
Alzheimer disease (AD) is the most frequent dementia. The prevalence is approximately 10% in 65 years old people. The current treatment is only progression protective, therefore it is crucial to find a new diagnostic approach for diagnosing AD in early stage. We analysed a set of 55 patients by the drop coating deposition Raman spectroscopy with the goal to verify previously published high sensitivity of the AD spectroscopic diagnosis in cerebral spinal fluid (CSF) and to find a new diagnostic method for blood serum (BS). We optimized measurement conditions for BS. The results were evaluated by the cluster analysis and the principal component analysis. The small set of samples exhibited high sensitivity in both CSF and BS but that distinctly decreased in the whole set. The results for CSF were affected by the choice of the analysed spectral interval. The best for AD diagnose was the interval containing peaks at 980, 1080 and 1249 cm-1.The results for BS have been the most sensitive in the whole spectral range. They have low sensitivity but high specificity for AD (92%). The usage of neural networks has conversely high sensitivity and low specificity in both sets of samples of BS and CSF. Powered by TCPDF (
Atomic force microscopy in the region of biomacromolecules
Vančura, Martin ; Kopecký, Vladimír (advisor) ; Bednárová, Lucie (referee)
Atomic force microscopy (AFM) enables sample imaging at the micro and nanoscale. Recently, the method is applied to investigate biomacromolecules. Here, we describe the basic principles of AFM with a special emphasis for bioapplications. We tested experimental abilities of Alpha 300 - the Raman microscope with AFM/SNOM accessory from WITec company. The ability of AFM to study objects of cellular dimensions was demonstrated on erythrocytes and green algae Desmodesmus quadricauda. We were able to observe growing of lysozyme protein fibrils on day scale - from dimensions of seeds (~3 nm height) up to fibrils itself (3-10 nm height and 100 nm up to micrometers length). Subsequently, we observed separate protein molecules of thyroglobulin (~6 nm) and also γ-globulin (~3 nm). It seems plausible to image objects up to 2 nm dimensions by the given device with respect to the signal/noise ratio.
Never Born Proteins: Occurence and characterization of secondary structure motifs
Treťjačenko, Vjačeslav ; Hlouchová, Klára (advisor) ; Kopecký, Vladimír (referee)
An experimental study on randomly generated protein sequences can provide important insights into the origin and mechanism of secondary structure formation and protein folding. In this study we bring biophysical characterization of five protein sequences selected from the in silico generated library of random chains. The sequences were selected on the basis of bioinformatic analysis in order to find the candidates with the maximum potential to possess secondary structure. This study shows that the random polypeptide sequences form stable secondary structures and in some show the signs of tertiary structure, such as hydrophobic core formation and distinctive oligomerization pattern. While the work presented in this thesis is work in progress on a larger study, the data already demonstrate that unevolved protein sequence space provides a lot of potential for secondary and tertiary structure formation that awaits its characterization. Powered by TCPDF (
Characterization of proteins of 2'-5' oligoadenylate pathway by means of vibrational spectroscopy
Víšová, Ivana ; Kopecký, Vladimír (advisor) ; Bednárová, Lucie (referee)
The work concerns to structural characterization of two important proteins of 2'-5' oligoadenylate pathway participating in an immune response of organism to a viral infection. Studied proteins were ankyrin domain of mouse RNase L, the C-terminal part of human phosphodiesterase 12 and the complete human phosphodiesterase 12. The proteins were characterized by Raman spectroscopy, infrared spectroscopy, electronic circular dichroism, dynamic light scattering and in addition by two non-spectroscopic methods- differential calorimetry and electrophoresis. For each protein the secondary structures, thermal stability, weight of oligomers and generally a basic characterization by above mentioned methods were provided.
Study of nucleic acids by means of drop coating deposition Raman microspectroscopy (DCDR)
Souček, Pavel ; Kopecký, Vladimír (advisor) ; Mojzeš, Peter (referee)
The work was focused on possibilities of the new technique of nonresonance Raman spectroscopy - drop coating deposition Raman (DCDR) spectroscopy upon study of nucleic acids. DCDR spectroscopy is based on deposition of a small droplet of the studied sample on a hydrophobic surface, where after evaporation of the solvent, ring of the studied material in glass phase is formed. That way the material is concentrated and upon measurements by means of Raman microspectrometry the increase of signal of several orders of magnitude is observed with respect to the standard technique of sample measurements in solvent. In this work we studied behavior of DNA 12-mer and DNA with 3000 base pairs. Our research showed that DCDR spectra of DNA dissolved in deionized water can be measured up to concentration of 30 M per base. The DCDR spectra are similar to those measured from solvents. Nevertheless, the deposited sample never forms a ring. It was shown that the size of nucleic acids didn't play dominant role upon ring formation but their charge which lead to repulsion of the molecules. After adding of sodium ions and subsequently also magnesium ions the ring formation was observed. Factor analysis of spectral maps demonstrated that formed rings are not fully homogenous and that upon their origin condensation of DNA could...
Spectroscopic study of interaction of antimicrobial peptides with model membranes
Tesař, Adam ; Kopecký, Vladimír (advisor) ; Kočišová, Eva (referee)
Antimicrobial peptides (AMP) have a great potential in medicine and pharmacy. Mechanism of their impact is an interaction with a cell membrane leading to the penetration of the membrane. The way of disruption of the cell membrane is not completely understand, therefore we focused on the interaction of AMP HAL-1, isolated from the venom of the bee Halictus sexctinctus, with a model membrane of 100 nm liposomes consisting of phosphatidylcholin and phosphatidylglycerol. Circular dichroism and infrared spectroscopy (FTIR) proved the change of the secondary structure from the random coil of free HAL-1 to -helix in an interaction with the membrane. The next step was preparation of the lipid bilayer on the surface of ATR prism, which will enable usage of the polarized FTIR spectroscopy to study the interaction of AMP with model membranes in future. Therefore, the ATR-FTIR spectroscopy and factor analyses were applied to study dynamics of drying of the liposomes and their subsequent hydration also with an addition of HAL-1. We focused on the stabilization of the system. Hydratation of the lipid bilayer by 2 µl sample showed stability for minutes, nevertheless after dilution the stabilization decay in minutes. The protective influence of the peptide on the lipid bilayer and slowing down of the drying out of the...
Diagnostics of neurodegenerative diseases by means of Raman spectroscopy
Klener, Jakub ; Kopecký, Vladimír (advisor) ; Matějka, Pavel (referee)
Therapies of neurodegenerative diseases are often very difficult and their success depend on an early diagnose. From that reason we have been developing new diagnostic method for multiple sclerosis and Alzheimer disease by drop coating deposition Raman (DCDR) spectroscopy of cerebrospinal fluid (CSF) in this work. We found out conditions of measurements, where spectra were reproducible and accepted for standard diagnostic practices. We discovered that CSF has fast degradation at a room temperature, which was detectable in spectra after 5 hours, and degradation due to refreezing. DCDR spectra of CSF from individual patients were analyzed by factor and cluster analysis. Multiple sclerosis was manifested by lower intensity of a Raman band at 1080 cm−1 , which is probably connected with more general pathologic state. Spectral changes caused by Alzeheimer disease were more complex and beside changes mentioned above also changes connected with composition and conformation of proteins were identified in regions 1200-1800 cm−1 and 2870-2950 cm−1 . Additionally, we succeeded in distinguishing of young healthy patients from older patients in DCDR spectra. In this work were checked up, that DCDR is good diagnostic method for clinical practices for determining neurodegenerative diseases through the complex...

National Repository of Grey Literature : 42 records found   1 - 10nextend  jump to record:
See also: similar author names
1 Kopecký, V.
3 Kopecký, Vojtěch
3 Kopecký, Václav
1 Kopecký, Vít
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